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Thursday, September 30, 2010

We had cupcakes to celebrate my advisor's birthday, and they were, in my opinion, unsatisfying. The cake was oily and lacked flavor, and the frosting was extremely thick, greasy and too sweet. As luck would have it, I saw this article on NPR about the rise of the cupcake. What I really like about the article is the list of recipes at the bottom. I will definitely be testing out a black bean or chickpea cupcake soon.

I cooked the beets from the last two weeks, and am not yet sure what I'm going to do with them.

As penance for deleting this week's photos I decided to go ahead and make these sweet potato muffins. However, I didn't have maple syrup, or applesauce, and had some stuff to use up in the cabinet/fridge so here is the recipe I really used:

Instructions are about the same for the recipe above, mix dry stuff together, wet stuff together, then mix both until smooth and put in muffin cups.

Sprinkle the tops of the muffins with 1tsp of granulated sugar, shared between all 12.

They're pretty tasty, and although there is the 2Tbs of oil, they are lower sugar. I'm sure you could leave out the oil and add more milk (or applesauce), I was just working with what I have here. I'll have to try the real recipe when I have all the ingredients!

Friday, September 24, 2010

I agree with him that the article was well-written but am a little concerned that it won't reach it's target audience. At the beginning of the article he states how poorly most commenters understood the basic science, and many are even "anti-science", but then goes on to discuss promoters and genes, with very little background. Even though I think he does a good job of clearly and concisely describing the technology, I think, for the majority of people, his explanation may still have too much substance without enough background.

For example, to keep some of his substance, it might have been useful to add that genes and promoters are different elements in the genome that work together, with a promoter serving as the "director", telling a gene when to be turned on or off, as well as how much product to produce. Switching promoters can change when and where a gene is expressed. During domestication, we select animals that have accumulated mutations in promoters (and genes) to give the physical qualities we are looking for. With this technology, rather than taking several hundreds or even thousands of years, we can select the sequences we want using tools in a laboratory.

We rented My Name Is Khan earlier this week. It is a long movie, but keeps your interest, and it is a very moving story about an man with Asperger Syndrome who moves to America, and is muslim. It shows his life both before and after 9/11/2001.

My uncle, aunt and their daughter are muslim.

They are not terrorists.

In a related vein, my Aunt posted this website, encouraging people to pray for peace for 1 minute each day until either the 10th anniversary of 9/11/2001 or the International Day of Peace (on 9/21/11). I think the sentiment behind the website is well-meaning but misguided. I would love to see a site promoting actions for peace. Although, I could buy the argument that prayer, like meditation, may help calm an individual's mind, and make that one person more likely to work towards peace in other events. But in the long run, it is the sum of small actions, patience and understanding that promote peace.

A few ideas for small actions to promote peace each day:
- read about customs from a culture foreign to you
- hold a door open, or an elevator
- smile, nod, wave when walking down the hall, or walking the dogs
- offer someone your seat
- let the person with 2 items in line behind you go first

The power to do good things doesn't come from any particular culture or any religion. The power to do good things is an independent choice. One thing we must remember is that although there are similarities, "good things" may vary dramatically from culture to culture. We can only hope to be the best people, for who and where we are right now. No one is perfect, nor can we expect perfection of ourselves, but we can expect the best of ourselves.

Wednesday, September 22, 2010

2010 PAWS Pet Extravaganza

Sunday, September 26, 11 am to 4 pm, at Penn State's Snider Ag Arena

Centre County PAWS is holding its 11th annual Pet Extravaganza on Sunday, September 26, 2010, 11 am to 4 pm, at Penn State's Snider Ag Arena. Admission is free, although donations are encouraged and appreciated. Pets are welcome as long as they are on leashes or in carriers and have proof of a current rabies vaccination.

Select PAWS cats and dogs will be present and adoption applications will be available. Dogs will be in the main arena. Cats will be in the main area and in a separate "cat room" near the front entrance.

This year's Pet Extravaganza will once again have a rabies vaccination clinic, microchip clinic, many interesting demonstrations, a variety of fun and educational contests and events, silent auction, and raffle. There will also be demonstrations from John P. Jones Canine Training, and a Kid's Corner with face painting and games!

Raffle prizes include a hot air balloon ride from The Sky's the Limit Ballooning; A Toftrees Golf Package for two; a 14-karat yellow gold Nittany Lion Bracelet; and two PSU football tickets for the game against Northwestern on November 6th. You don't need to be present to win these great prizes and one ticket is only $2!

I've been writing/researching quite a lot the past week, and it'll probably be a little sparse around here until November.

Over the past week I've submitted three fellowship applications (yay!), and have a good draft to work from for submitting two more fellowships and a smaller grant application (for supplies). It feels good to have three down and three to go - although one of the three to go is the NIH postdoctoral fellowship, which is quite involved. The fellowships are due mid-Oct and early-Nov, and the mini-grant isn't due till January.

Also, after talking with one of my mentors yesterday, he suggested three other fellowships I could potentially apply for (due Feb, March and June). If the people writing my reference letters aren't completely sick of me by then, perhaps I'll try to submit to a couple of these as well! I'm starting to get very optimistic that I'll be able to find funding for my postdoc now. I'll try to ride this wave until March when I start hearing back from them. :)

Last week I also wrote and submitted an article for the GWIS E-newsletter about one of our past GWIS fellowship winners. I will be writing a few more of these to be included as a regular section, and was invited to write the cover-article for the Spring GWIS Bulletin about our past fellowship winners. The due date for that isn't until Spring, but I'm hoping to have all of these done before the beginning of December.

This week I'm putting together the outline for a review of Male Mutation Bias. The challenge here is to focus on papers submitted in just the past 3 years, but being in the field, I know of a few that are only in preparation - I hope they come out so I can include them in the review!

I'm also hoping to get one on my research papers in near-final form this week, or early next week, to submit to our collaborators for their approval.

So, lots and lots of writing, but I'll try not to be too neglectful.

On the baby-front, we had a check-up yesterday. We're at 27 weeks and I'm up 22lbs. I'm hoping to reign it in a little, but She's growing and has a healthy heartbeat, so all seems to be well. She has started kicking with a little more enthusiasm, although not more regularly, so I haven't had the opportunity to force any of my friends to feel her move. I'm sure that'll happen soon enough though. :)

I'm not yet sure what to make with everything. I am slipping a little with the adventurous recipes. Tonight we're finishing the chicken soup we made last week. This weekend I did experiment with the whole wheat pizza dough, and sliced pears spiced with cinnamon, for a delicious breakfast tart:

Just peel and slice 2 pears, mix with 2tsp sugar and 2 tsp cinnamon. After making dough, spread in two sheets, smear with 1Tbs butter, and arrange pear mixture on each. Bake at 350 for 10-12 minutes or until desired crispness of crust.

Monday, September 13, 2010

This weekend's Bioinformatics and Genomics (BG) retreat went very well! We had over 60 faculty and students make oral and poster presentations, share ideas and get to know one another. It was especially useful for me to connect with a couple of faculty with whom I would like to discuss ideas for my research proposal.

This morning I drove around dropping off sponsorship letters to local businesses, requesting donations for the upcoming USA Science and Engineering Festival. We are planning to teach polymer science to kids who stop by our booth. The Festival estimates 100,000 people on the mall, and about 10,000 people stopping by each booth!! Whew!

This weekend I was also able to finish some analysis on one of my current projects (male mutation bias), and although the results are a little puzzling right now, it is nice to have the results to look at and interpret.

I'm going to devote a lot of time this week to writing: writing manuscripts, writing research proposals, writing a letter of recommendation for an undergrad professor of mine, writing the background for a review article.

I have five fellowship/grant applications to finish in the text two months, and a sixth due in January, and it's starting to get a wee bit stressful (just a little though). Mostly just nerves, so it'll be good to get them done and out of the way.

Thursday, September 9, 2010

I used the lettuce in a taco salad for dinner tonight. We grilled a couple ears of corn last night to eat with the rest of our boiled kobacha squash. I tried to toast the seeds of the kobacha squash, but they're a bit different from pumpkin seends. They started popping (like popped corn) in the oven, so I quickly took them out before I wanted. And, the meaty parts of the seeds sticks to the hulls. My final opinion is that they are a bit more work than they're worth.

Wednesday, September 8, 2010

I really do try to get here every day, but it seems the days are slipping past and now it is Wednesday already.

We picked up our veggies yesterday - so look for a post soon about them!

Today my labmate, Yogeshwar, defended his thesis. Well, he's currently in the private portion of the defense, but I'm confident he'll be successful. So, here's a premature "Congratulations!" to Dr. Yogeshwar Kelkar.

I'll be a bit busier this week than usual because I'm working to get some results for my advisor before she leaves for a conference this weekend. Even with staying up late last night, I still feel behind, so am expecting a couple more late nights. Still, I hope to finish up and be able to have a couple decent posts for you this week.

We made salsa with most of the tomatoes, onion, garlic, peppers (hot and mild), adding just a little lime juice. We grilled the eggplant with just a little salt and pepper, and steamed the green beans.

The watermelons were both perfectly ripe, sweet and juicy.

I haven't yet cooked the squash, but am really looking forward to it. I'm not sure yet about roasting it, or making a soup. We'll see....

And tonight I had a bunch of leftover stuff in the cabinets and came up with a new dessert (mainly because I was out of butter and my can of evaporated milk was solid when I opened the can). This is a homemade graham cracker crust with a filling of chocolate, coconut, chopped oats and a little milk to make it chewy. They were a good afternoon treat for Scott and our friends Brian and Amanda, after they went out mountain biking. I think they're tasty with a cup of hot tea.

Friday, September 3, 2010

Part of my goal with this accessible research is to introduce you, dear readers, to some topics you might otherwise overlook because they seem uninteresting, irrelevant, or just unaccessible. Many apologies to the scientists' whose research I paraphrase if you come across my blog and think I've over-simplified, or somehow mis-represented your results. That is certainly not my intention - and I welcome your comments!

Also, may thanks for putting up with my very lame, and sometimes obscure, sense of humor. :) Today's title was chosen because the I thought the tagline for Fast Times at Ridgemont High fit well:

Noncoding sequences are DNA sequences that do not code for a protein. Most of what is discussed in the mainstream media is coding sequence. Generally, when a gene is discussed, we are actually referring to the protein it produces; this protein is made from the coding sequence of the gene.

So why do we care about how noncoding sequence evolves? The noncoding sequences can be very useful because they can contain signals that tell the protein how to fold, tell the gene when and where to be expressed, and how much should be produced. For example, in typing this, I'm pretty glad that signals were given to make sure that cells in my heart differentiated properly into the right kind of muscle tissue to be able to pump blood through my body, while the cells in the back of my eyeballs developed light-receptors, instead of the other way around. There are still so many factors both genetic and environmental) that determine how tissues differentiate, and what genes are expressed when, but one way to get a handle on this is to look at how the noncoding sequence evolves.

In particular, these researchers looked at the noncoding sequence around genes that have duplicated - that is, there are two copies of these genes in our genome.

If both are retained, it is likely that one, or both copies evolved a new function (See Hughes, 2005 in PNAS for a short review). The new function could have come from changes in the coding sequence (changing the protein itself, and therefore what it does), or could have come from changes in the noncoding region (potentially changing the timing, location or abundance of the protein produced).

Here it is good to mention that many genes have more than just one function, and may be expressed in many tissues, performing different functions based on the tissues in which they are expressed. So, it is expected that changes in the noncoding region may have a large impact on the gene. These changes may be responsible for many of the differences observed between species.

Indeed, these Kostka, Hahn and Pollard (2010) found that the noncoding regions around duplicate genes (duplicated only in humans & chimpanzees after their divergence from macaque) evolve faster than the noncoding regions around single-copy genes (that are single copy in human and macaque). Both this study, and a similar one by Park and Makova (2009), show that noncoding sequences around duplicate genes evolve quite rapidly, complementing work by Chung et al., (2006), which found that the coding sequence of duplicate genes also evolves rapidly.

The current study goes further to look at the functions of the genes nearby the noncoding sequence and finds that many of them are expressed during pregnancy and the formation of the placenta.

So, while my little bun in the oven kicks to remind me she's working hard on developing, I now know the sequence likely involved in regulating the formation of her protective placenta has evolved pretty rapidly over the past few million years, and, although it still needs to be tested, hopefully it is due to selection on beneficial mutations (stay safe in there little one!).

I haven't taken pictures of them yet, but our friends were so sweet as to can some of the veggies, so we now have two jars of dilly beans (pickled green beans) and a jar of homemade spicy spaghetti sauce to enjoy!

I took a picture of this week's share and will do my best to get it posted later today.

Wired: Why is it so hard to convince people, even when the science is so clear?

Simon Singh: Science has nothing to do with common sense. I believe it was Einstein who said that common sense is a set of prejudices we form by the age of 18. Inject somebody with some viruses and that’s going to keep you from getting sick? That’s not common sense. We evolved from single-cell organisms? That’s not common sense. By driving my car I’m going to cook Earth? None of this is common sense. The commonsense view is what we’re fighting against. So somehow you’ve got to move people away from that with these quite complicated scientific arguments based on even more complicated research. That’s why it’s such an uphill battle. People start off with a belief and a prejudice—we all do. And the job of science is to set that aside to get to the truth.

Of course, here, I'll be biased towards science that I am more familiar with, but you'll just have to put up with that for now.

In the next installment of tasty tid-bits for your brain, I'll look at a paper published in GBE, that you can view here, open access. (Gotta love open access!)

Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study

Gabriel A. B. Marais*,1, Paulo R. A. Campos2 and Isabel Gordo3

Genome Biology and Evolution Vol. 2:347; doi:10.1093/gbe/evq026

The title is pretty informative to someone in the field, but you might be wondering: Why is the Y degenerating? What do I care if it is lost? And what is gene conversion?

Well, to understand why the Y is degenerating, we need to know where it came from. In humans the X and Y chromosomes are called the sex chromosomes. Females have two X chromosomes (XX) and males have one of each (XY). In mammals sex, and specifically maleness, is determined genetically by a gene on the Y chromosome. The X and Y were originally identical to each other, but after the Y gained this male-determining gene, it started to become a male-specific chromosome, losing most (97%) of its genes! Whereas the X and Y used to recombine (swap bits of DNA) in order to fix mutations and deletions, the Y now is mostly non-recombining. This means that deletions and errors on the Y cannot be fixed by partnering with the X - it is a lonely chromosome.

Some people have wondered: What mechanisms help the degenerated Y stick around? Because it cannot recombine (to fix errors) why doesn't it just lose all of its content? The authors here run computer simulations to try and answer this very question.

We need to bring one up more bit of background - even with all of the degeneration and gene loss on the Y chromosome, there has been substantialgene gain in one particular region: the ampliconic region. This region is made of palindrome (yes, exactly like Madam I'm Adam - the same forward and backwards) of long repeated gene regions. Think:

Palindrome = Copy1.Copy2.Copy3.-.3ypoC.2ypoC.1ypoC

These researchers wondered whether pairing and sharing between the identical regions of each palindrome might serve as a mechanism to retain gene content on the Y chromosome. And, indeed, they found that this was true in their simulations!

So, it seems like, even though the Y has degraded quite a bit, it may have figured out a loophole, a way to keep from being lost forever. Good news for all those worried guys out there - looks like you'll be keeping your male-determining chromosome for a little while longer. :)

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